biotechnology (10)

Soap-Like Properties...

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1 Soap, shampoo, and worm-like micelles Soaps and shampoos are made from amphiphilic molecules with water-loving (red) and water-hating (blue) parts that arrange themselves to form long tubes known as “worm-like micelles”. Entanglements between the tubes give these materials their pleasant, sticky feel. b The micelles can, however, disentangle themselves, just as entangled long-chain polymer molecules can slide apart too. In polymers, this process can be modeled by imagining the molecule sliding, like a snake, out of an imaginary tube formed by the surrounding spatial constraints. c Worm-like micelles can also morph their architecture by performing reconnections (left), breakages (down), and fusions (right). These operations occur randomly along the backbone, are in thermal equilibrium, and are reversible. (Courtesy: Davide Michieletto)

Topics: Biology, Biotechnology, DNA, Molecules

DNA molecules are not fixed objects – they are constantly getting broken up and glued back together to adopt new shapes. Davide Michieletto explains how this process can be harnessed to create a new generation of “topologically active” materials.

Call me naive, but until a few years ago I had never realized you can actually buy DNA. As a physicist, I’d been familiar with DNA as the “molecule of life” – something that carries genetic information and allows complex organisms, such as you and me, to be created. But I was surprised to find that biotech firms purify DNA from viruses and will ship concentrated solutions in the post. In fact, you can just go online and order DNA, which is exactly what I did. Only there was another surprise in store.

When the DNA solution arrived at my lab in Edinburgh, it came in a tube with about half a milligram of DNA per centimeter cube of water. Keen to experiment with it, I tried to pipette some of the solutions out, but they didn’t run freely into my plastic tube. Instead, it was all gloopy and resisted the suction of my pipette. I rushed over to a colleague in my lab, eagerly announcing my amazing “discovery”. They just looked at me like I was an idiot. Of course, solutions of DNA are gloopy.

I should have known better. It’s easy to idealize DNA as some kind of magic material, but it’s essentially just a long-chain double-helical polymer consisting of four different types of monomers – the nucleotides A, T, C, and G, which stack together into base pairs. And like all polymers at high concentrations, the DNA chains can get entangled. In fact, they get so tied up that a single human cell can have up to 2 m of DNA crammed into an object just 10 μm in size. Scaled up, it’s like storing 20 km of hair-thin wire in a box no bigger than your mobile phone.

Make or break: building soft materials with DNA, Davide Michieletto is a Royal Society university research fellow in the School of Physics and Astronomy, University of Edinburgh, UK

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RNA and Covid-19...

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NIST researcher Megan Cleveland uses a PCR machine to amplify DNA sequences by copying them numerous times through a series of chemical reactions.
Credit: M. Cleveland/NIST

Topics: Biology, Biotechnology, COVID-19, Diversity in Science, NIST, Research, Women in Science

Scientists track and monitor the circulation of SARS-CoV-2, the virus that causes COVID-19, using methods based on a laboratory technique called polymerase chain reaction (PCR). Also used as the “gold standard” test to diagnose COVID-19 in individuals, PCR amplifies pieces of DNA by copying them numerous times through a series of chemical reactions. The number of cycles it takes to amplify DNA sequences of interest so that they are detectable by the PCR machine, known as the cycle threshold (Ct), is what researchers and medical professionals look at to detect the virus.

However, not all labs get the same Ct values (sometimes also called “Cq” values). In efforts to make the results more comparable between labs, the National Institute of Standards and Technology (NIST) contributed to a multiorganizational study that looked at anchoring these Ct values to a reference sample with known amounts of the virus.

Researchers published their findings in the journal PLOS One.

SARS-CoV-2 is an RNA virus: Its genetic material is single-stranded instead of double-stranded like DNA and contains some different molecular building blocks, namely uracil in place of thymine. But the PCR test only works with DNA, and labs first must convert the RNA to DNA to screen for COVID-19. For the test, RNA is isolated from a patient’s sample and combined with other ingredients, including short DNA sequences are known as primers, to transform the RNA into DNA.

RNA Reference Materials Are Useful for Standardizing COVID-19 Tests, Study Shows, NIST

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ACE2 Gum and Covid...

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Visual Abstract

Topics: Biology, Biotechnology, COVID-19, Research

To advance a novel concept of debulking virus in the oral cavity, the primary site of viral replication, virus-trapping proteins CTB-ACE2 were expressed in chloroplasts and clinical-grade plant material was developed to meet FDA requirements. Chewing gum (2 g) containing plant cells expressed CTB-ACE2 up to 17.2 mg ACE2/g dry weight (11.7% leaf protein), have physical characteristics and taste/flavor like conventional gums, and no protein was lost during gum compression. CTB-ACE2 gum efficiently (>95%) inhibited entry of lentivirus spike or VSV-spike pseudovirus into Vero/CHO cells when quantified by luciferase or red fluorescence. Incubation of CTB-ACE2 microparticles reduced SARS-CoV-2 virus count in COVID-19 swab/saliva samples by >95% when evaluated by microbubbles (femtomolar concentration) or qPCR, demonstrating both virus trapping and blocking of cellular entry. COVID-19 saliva samples showed low or undetectable ACE2 activity when compared with healthy individuals (2,582 versus 50,126 ΔRFU; 27 versus 225 enzyme units), confirming greater susceptibility of infected patients for viral entry. CTB-ACE2 activity was completely inhibited by pre-incubation with SARS-CoV-2 receptor-binding domain, offering an explanation for reduced saliva ACE2 activity among COVID-19 patients. Chewing gum with virus-trapping proteins offers a generally affordable strategy to protect patients from most oral virus re-infections through debulking or minimizing transmission to others.

Debulking SARS-CoV-2 in saliva using angiotensin-converting enzyme 2 in chewing gum to decrease oral virus transmission and infection, Molecular Therapy: Cell.com

Henry Daniell, Smruti K. Nair, Nardana Esmaeili, Geetanjali Wakade, Naila Shahid, Prem Kumar Ganesan, Md Reyazul Islam, Ariel Shepley-McTaggart, Sheng Feng, Ebony N. Gary, Ali R. Ali, Manunya Nuth, Selene Nunez Cruz, Jevon Graham-Wooten, Stephen J. Streatfield, Ruben Montoya-Lopez, Paul Kaznica, Margaret Mawson, Brian J. Green, Robert Ricciardi, Michael Milone, Ronald N. Harty, Ping Wang, David B. Weiner, Kenneth B. Margulies, Ronald G. Collman

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Wearable Pressure Sensor...

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Hybrid device: A diagram of the layers in the new soft pressure sensor. (Courtesy: the University of Texas at Austin)

Topics: Applied Physics, Biotechnology, Nanotechnology

Wearable pressure sensors are commonly used in medicine to track vital signs, and in robotics to help mechanical fingers handle delicate objects. Conventional soft capacitive pressure sensors only work at pressures below 3 kPa, however, meaning that something as simple as tight-fitting clothing can hinder their performance. A team of researchers at the University of Texas has now made a hybrid sensor that remains highly sensitive over a much wider range of pressures. The new device could find use in robotics and biomedicine.

The most common types of pressure sensors rely on piezoresistive, piezoelectric, capacitive, and/or optical mechanisms to operate. When such devices are compressed, their electrical resistance, voltage, capacitance, or light transmittance (respectively) changes in a well-characterized way that can be translated into a pressure reading.

The high sensitivity and long-term stability of capacitive pressure sensors make them one of the most popular types, and they are often incorporated into soft, flexible sensors that can be wrapped around curved surfaces. Such sensors are popular in fields such as prosthetics, robotics, and biometrics, where they are used to calibrate the strength of a robot’s grip, monitor pulse rates, and blood pressure, and measure footstep pressure. However, these different applications involve a relatively wide range of pressures: below 1 kPa for robotic electronic skin (e-skin) and pulse monitoring; between 1 and 10 kPa for manipulating objects; and more than 10 kPa for blood pressure and footstep pressure.

Wearable pressure sensors extend their range, Isabelle Dumé, Physics World

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Steve Austin's Beads...

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Magnetic prosthetic: A magnetic sensing array enables a new tissue tracking strategy that could offer advanced motion control in artificial limbs. (Courtesy: MIT Media Lab/Cameron Taylor/Vessel Studios)

Topics: Biotechnology, Magnetism, Materials Science, Medicine, Nanotechnology, Robotics

Cultural reference: The Six Million Dollar Man, NBC

In recent years, health and fitness wearables have gained popularity as platforms to wirelessly track daily physical activities, by counting steps, for example, or recording heartbeats directly from the wrist. To achieve this, inertial sensors in contact with the skin capture the relevant motion and physiological signals originating from the body.

As wearable technology evolves, researchers strive to understand not just how to track the body’s dynamic signals, but also how to simulate them to control artificial limbs. This new level of motion control requires a detailed understanding of what is happening beneath the skin, specifically, the motion of the muscles.

Skeletal muscles are responsible for almost all movement of the human body. When muscle fibers contract, the exerted forces travel through the tendons, pull the bones, and ultimately produce motion. To track and use these muscle contractions in real-time and with high signal quality, engineers at the Massachusetts Institute of Technology (MIT) employed low-frequency magnetic fields – which pass undisturbed through body tissues – to provide accurate and real-time transcutaneous sensing of muscle motion. They describe their technique in Science Robotics.

Magnetic beads inside the body could improve control of bionic limbs, Raudel Avila is a student contributor to Physics World

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The Anatomy of Delta...

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A computer simulation of the structure of the coronavirus SARS-CoV-2.Credit: Janet Iwasa, University of Utah

Topics: Biology, Biotechnology, COVID-19, DNA, Existentialism, Research

The coronavirus sports a luxurious sugar coat. “It’s striking,” thought Rommie Amaro, staring at her computer simulation of one of the trademark spike proteins of SARS-CoV-2, which stick out from the virus’s surface. It was swathed in sugar molecules, known as glycans.

“When you see it with all the glycans, it’s almost unrecognizable,” says Amaro, a computational biophysical chemist at the University of California, San Diego.

Many viruses have glycans covering their outer proteins, camouflaging them from the human immune system like a wolf in sheep’s clothing. But last year, Amaro’s laboratory group and collaborators created the most detailed visualization yet of this coat, based on structural and genetic data and rendered atom-by-atom by a supercomputer. On 22 March 2020, she posted the simulation to Twitter. Within an hour, one researcher asked in a comment: what was the naked, uncoated loop sticking out of the top of the protein?

Amaro had no idea. But ten minutes later, structural biologist Jason McLellan at the University of Texas at Austin chimed in: the uncoated loop was a receptor-binding domain (RBD), one of three sections of the spike that bind to receptors on human cells (see ‘A hidden spike’).

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Source: Structural image from Lorenzo Casalino, Univ. California, San Diego (Ref. 1); Graphic: Nik Spencer/Nature

How the coronavirus infects cells — and why Delta is so dangerous, Megan Scudellari, Nature

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Smart Foam...

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A robotic hand with the AiFoam artificially innervated smart foam, which enables it to sense objects in proximity by detecting their electrical fields and also self-heals if it gets cut, is pictured at National University Singapore's Materials Sciences and Engineering lab in Singapore June 30, 2021. REUTERS/Travis Teo

Topics: Biology, Biotechnology, Materials Science, Polymer Science, Robotics

SINGAPORE, July 6 (Reuters) - Singapore researchers have developed a smart foam material that allows robots to sense nearby objects, and repairs itself when damaged, just like human skin.

Artificially innervated foam, or AiFoam, is a highly elastic polymer created by mixing fluoropolymer with a compound that lowers surface tension.

This allows the spongy material to fuse easily into one piece when cut, according to researchers at the National University of Singapore.

"There are many applications for such a material, especially in robotics and prosthetic devices, where robots need to be a lot more intelligent when working around humans," explained lead researcher Benjamin Tee.

To replicate the human sense of touch, the researchers infused the material with microscopic metal particles and added tiny electrodes underneath the surface of the foam.

Smart foam material gives robotic hand the ability to self-repair, Travis Teo, Lee Ying Shan, Reuters Science

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Quantum Microscope...

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Artist’s impression of UQ’s new quantum microscope in action. Credit: The University of Queensland

Topics: Biology, Biotechnology, Instrumentation, Quantum Mechanics, Quantum Optics

In a major scientific leap, University of Queensland researchers have created a quantum microscope that can reveal biological structures that would otherwise be impossible to see.

This paves the way for applications in biotechnology, and could extend far beyond this into areas ranging from navigation to medical imaging.

The microscope is powered by the science of quantum entanglement, an effect Einstein described as “spooky interactions at a distance.”

Professor Warwick Bowen, from UQ’s Quantum Optics Lab and the ARC Centre of Excellence for Engineered Quantum Systems (EQUS), said it was the first entanglement-based sensor with performance beyond the best possible existing technology.

“This breakthrough will spark all sorts of new technologies — from better navigation systems to better MRI machines, you name it,” Professor Bowen said.

“Entanglement is thought to lie at the heart of a quantum revolution. We’ve finally demonstrated that sensors that use it can supersede existing, non-quantum technology.

“This is exciting — it’s the first proof of the paradigm-changing potential of entanglement for sensing.”

Major Scientific Leap: Quantum Microscope Created That Can See the Impossible, University of Queensland

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Pandora's Box...

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MS TECH / SOURCE PHOTO: GETTY

 

Topics: Biology, Biotechnology, Civics, Ethics, Existentialism


A private DNA ancestry database that’s been used by police to catch criminals is a security risk from which a nation-state could steal DNA data on a million Americans, according to security researchers.

Security flaws in the service, called GEDmatch, not only risk exposing people’s genetic health information but could let an adversary such as China or Russia create a powerful biometric database useful for identifying nearly any American from a DNA sample.

GEDmatch, which crowdsources DNA profiles, was created by genealogy enthusiasts to let people search for relatives and is run entirely by volunteers. It shows how a trend toward sharing DNA data online can create privacy risks affecting everyone, even people who don’t choose to share their own information.

“You can replace your credit card number, but you can’t replace your genome,” says Peter Ney, a postdoctoral researcher in computer science at the University of Washington.

Ney, along with professors and DNA security researchers Luis Ceze and Tadayoshi Kohno, described in a report posted online how they developed and tested a novel attack employing DNA data they uploaded to GEDmatch.

 

The DNA database used to find the Golden State Killer is a national security leak waiting to happen
Antonio Regalado, Technology Review

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Decoding Sweat...

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New wearable sensors developed by scientists at UC Berkeley can provide real-time measurements of sweat rate and electrolytes and metabolites in sweat. (Credit: Bizen Maskey, Sunchon National University)

 

Topics: Biophysics, Biotechnology, Microfluidics, Nanotechnology, Research


A new scalable, high-throughput fabrication process that makes use of roll-to-roll printing and laser cutting can produce wearable sweat sensors rapidly and reliably and on a large scale. The devices, which can almost instantly detect and analyse electrolytes, metabolites and other biomolecules contained in sweat, could be employed in real-world applications and not just as laboratory prototypes.

Analyzing sweat is a non-invasive way to monitor a range of biomolecules, from small electrolytes to metabolites and hormones and larger proteins that come from deeper in the body. Indeed, sweat sensing has already been used to medically diagnose diseases like cystic fibrosis and autonomic neuropathy and to assess fluid and electrolyte balance in endurance athletes.

Traditional sweat sensors collect sweat from the body at different times and then analyse it. This means that the devices can’t be used to detect real-time changes in sweat composition – during physical activity, for example, or to monitor glucose levels in diabetic patients. Wearable sensors, which make use of flexible and hybrid electronics, overcome this problem by allowing for in-situ sweat measurements with real-time feedback. However, it is still difficult to reliably make sweat sensor components (including microfluidic chip and sensing electrodes) in large quantities and with good reproducibility.

 

Wearable patches could ‘decode’ sweat, Belle Dumé, Physics World

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